This is the documentation website for the TreeNode R package.
TreeNode is a library for reading, writing and manipulating phylogenetic trees in C# and R. It can open and create files in the most common phylogenetic formats (i.e. Newick/New Hampshire and NEXUS) and adds support for two new formats, the Newick-with-Attributes and Binary format.
The TreeNode R package can be used to read and write files in these two formats. The tree produced by this package have the same structure (and, thus, are compatible with) the popular phylogenetics package ape.
TreeNode is released under the GPLv3 licence.
Getting started
You can install the TreeNode R package from GitHub using the install_github function provided by the package devtools.
First, install devtools (if you have not done so already):
install.packages("devtools")
Then, you can install TreeNode by using the following command:
devtools::install_github("arklumpus/TreeNode/R")
Usage
The TreeNode R package provides functions to read and write phylogenetic trees in the NWKA and binary formats.
The read_nwka_tree() function can be used to read a file (or a string) containing tree(s) in NWKA format. The read_nwka_nexus() function can be used to read files in NEXUS format, interpreting the trees that they contain as NWKA trees.
The read_binary_trees() function can be used to read a file in binary format. The read_one_binary_tree() function can be used to read just one tree from the file.
The write_nwka_tree() function can be used to create a NWKA or Newick file (or string) starting from a phylo or multiPhylo object. The write_nwka_nexus() function can be used to create a NEXUS file in which the trees are stored in NWKA format.
The write_binary_trees() function can be used to create a tree file in binary format starting from a phylo or multiPhylo object. The begin_writing_binary_trees(), keep_writing_binary_trees() and finish_writing_binary_trees() functions can be used to write one tree at a time to the file.
Detailed documentation and examples for this package are available in the R online help (e.g., by typing ?read_nwka_tree at the R prompt) or in the function description pages.